1. Field of the Invention
The present invention relates to a robust method of identifying whether a target nucleic acid is a wild type or a mutant type using a DNA chip.
2. Description of the Related Art
The most common genotyping method is to identify sequences using sequencing machine. This method is accurate but is unsuitable for genotyping a number of samples at a time and leads to a low yield.
Recent disclosures of DNA chips that can simultaneously identify various genotypes at different positions, such as U.S. Pat. Nos. 6,027,880 and 6,300,063, are attracting a lot of interest. The DNA chips disclosed in the patents utilize tiled arrays of from 9 to 24-mer oligonucleotide probes at non-mutation sites and A, C, G, and T at mutation sites. Since all possible base combinations are used for a tiled array of probes mobilized at and near mutation sites, the number of required probes increases four times whenever one more tiled array site is required.
However, such a tiled array includes redundant probes for an identified target nucleic acid. In addition, the tiled array method cannot applied to detect mutations, for example, by insertion or deletion. Since a tiled array includes numerous probes having similar sequences and a fixed length, it is difficult to interpret the results of genotyping a particular locus using such a tiled array, and the manufacturing costs of DNA chips rise. For example, if the hybridization intensity of a wild-perfect match probe or a mutant-perfect match probe is lower than the hybridization intensity of the other mismatch probes, a genotyping error occurs and it is not possible to prove a cross-hybridization effect. Also, the fixed length of the probes in the tiled array hinders optimal hybridization with a particular nucleic acid.